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Pear trees with severe early defoliation usually suffer from weakened aboveground growth and a serious decrease of fruit quality and yield. Soil fertility and its microbial community and functional activity are significant factors impacting plant growth and yield, which also might be the very factors that influence the early defoliation of pear trees. To address the problems caused by chemical fertilizers, bioorganic fertilizer (BIO) and silicon amendment (SOA) are increasingly used as amendments to improve soil microbial activity and increase soil nutrient availability. However, how effective BIO and SOA are at improving the health of soils and reducing early defoliation remains unclear. Here, we conducted a 4-year field experiment (2016–2019) in a 25-year-old 'Cuiguan' pear orchard in Jianning county, Fujian province, comparing local custom fertilization (CK), local custom fertilization supplemented with SOA (CK-SOA), BIO, and BIO supplemented with SOA (BIO-SOA). At the end of the 4-year study we found that BIO and BIO-SOA treatments resulted in reduced leaf nitrogen content and increased leaf potassium (K), calcium (Ca), silicon (Si), and manganese (Mn) content. BIO and BIO-SOA treatments also resulted in a 50% reduction of the early deciduous rate and a 47% increase in pear yield. Compared with CK treated soil, BIO and BIO-SOA treated soils had higher nitrate nitrogen content (NO 3 −-N), available Si, Fe, Mn, and Zn content, and significantly improved microbial biomass nitrogen content (MBN), geometric mean enzyme activity (GMEA) and ecosystem multifunctionality (EMF). Network analysis revealed that BIO and BIO-SOA treatments had significantly altered the bacterial and fungal community composition in the orchard soil. Redundancy analysis (RDA) and the Mantel test indicated that soil available K, exchangeable Ca and Mg, and available Si, Fe, Mn and Zn content were the main factors influencing bacterial and fungal communities. The increased nutrient availability (e.g., NO 3 −-N and microelement contents), MBN, GMEA and EMF had negative effects on the early defoliation rate. Random Forest model identified soil available Si content, microbial biomass nitrogen content, EMF, and GMEA as the main predictors of early defoliation rate. Overall, this study demonstrates that application of BIO or BIO mixed with SOA can alleviate the early defoliation rate of pear trees by increasing the availability of microelements, microbial functional activity, and changing the soil microbial community composition. [Display omitted] • BIO and BIO-SOA significantly reduced the early defoliation rate of pear trees, and improved the pear yield. • BIO and BIO-SOA significantly increased soil available Si, Fe, Mn and Zn concentrations in pear orchard. • Soil microelements (e.g. Mg, Si, Fe and Zn) availability strongly affects microbial communities. • Belowground interactions significantly affects the growth of aboveground parts of pear trees. [ABSTRACT FROM AUTHOR]